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a7404cdd91
* remove MMFF:setMMFFAromaticity() * remove AtomPairs.Utils.NumPiElectrons() * remove the deprecated DistGeom contrib files * document removed stuff
90 lines
2.9 KiB
C++
90 lines
2.9 KiB
C++
//
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// Copyright (C) 2024 Greg Landrum and other RDKit contributors
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <RDGeneral/export.h>
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#ifndef RD_CHIRALVIOLATIONCONTRIBS_H
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#define RD_CHIRALVIOLATIONCONTRIBS_H
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#include <vector>
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#include <ForceField/Contrib.h>
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#include <Geometry/point.h>
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namespace DistGeom {
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class ChiralSet;
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RDKIT_DISTGEOMETRY_EXPORT double calcChiralVolume(
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const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
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const unsigned int idx4, const double *pos, const unsigned int dim);
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RDKIT_DISTGEOMETRY_EXPORT double calcChiralVolume(
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const unsigned int idx1, const unsigned int idx2, const unsigned int idx3,
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const unsigned int idx4, const RDGeom::PointPtrVect &pts);
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struct ChiralViolationContribsParams {
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unsigned int idx1{0}, idx2{0}, idx3{0}, idx4{0};
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double volUpper{0.0};
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double volLower{0.0};
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double weight{1.0};
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ChiralViolationContribsParams(unsigned int i1, unsigned int i2,
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unsigned int i3, unsigned int i4, double u,
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double l, double w = 1.0)
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: idx1(i1),
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idx2(i2),
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idx3(i3),
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idx4(i4),
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volUpper(u),
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volLower(l),
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weight(w) {};
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};
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//! A term to capture the violation of chirality at atom centers
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//!
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class RDKIT_DISTGEOMETRY_EXPORT ChiralViolationContribs
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: public ForceFields::ForceFieldContrib {
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public:
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ChiralViolationContribs() = default;
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//! Constructor
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/*!
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\param owner pointer to the owning forcefield
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\param cset a chiral set containing the four chiral atom ids (in
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sequence)
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and the upper and lower limits on the signed chiral
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volume \param weight (optional) the weight to be used for this contrib
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*/
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ChiralViolationContribs(ForceFields::ForceField *owner);
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//! adds a new chiral constraint
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/*!
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\param cset a chiral set containing the four chiral atom ids (in
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sequence)
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and the upper and lower limits on the signed chiral
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volume \param weight (optional) the weight to be used for this contrib
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*/
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void addContrib(const ChiralSet *cset, double weight = 1.0);
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//! return the contribution of this contrib to the energy of a given state
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double getEnergy(double *pos) const override;
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//! calculate the contribution of this contrib to the gradient at a given
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/// state
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void getGrad(double *pos, double *grad) const override;
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ChiralViolationContribs *copy() const override {
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return new ChiralViolationContribs(*this);
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}
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bool empty() const { return d_contribs.empty(); }
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unsigned int size() const { return d_contribs.size(); }
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private:
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std::vector<ChiralViolationContribsParams> d_contribs;
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};
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} // namespace DistGeom
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#endif
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